|
| Status |
Public on Mar 05, 2022 |
| Title |
UPP Pathway Specific Mutants 3_S61 |
| Sample type |
SRA |
| |
|
| Source name |
Pooled G-DNA from cells in colonies
|
| Organism |
Agrobacterium fabrum str. C58 |
| Characteristics |
genotype: delta_uppW mutant alone
|
| Growth protocol |
Colonies with low UPP phenotype (low Congo Red staining) were cultured and pooled)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA extraction (Promega gDNA extraction kit))
DNA was sheared to 200-700 bp fragments. Terminal deoxynucleotidyl transferase (TdT) tailed. PCR was used to append bar-coded aptamers specific for transposon insertions followed by those required for Illumina sequencing. 1M SE reads per sample were generated on Illumina NextSeq500 sequencer using a 75 high cycle sequencing kit and a custom sequencing primer.
|
| |
|
| Library strategy |
Tn-Seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
GSF1944.S61.PoolTn-Seq
Illumina sequenced using transposon specific primers
|
| Data processing |
Reads were quality and adapter trimmed w/ Trimmomatic (v0.33; ILLUMINACLIP:adapters.fa:2:20:6 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:20)
For files GSF1864 and GSF1944, sequencing would begin in transposon and only reads starting with the expected AACCTGTTA sequence were kept
Reads were mapped to the Agrobacterium tumefaciens C58 genome using bowtie2 (v2-2.3.2) with default parameters other than allowing for 2 alignments with -k 2 option
After mapping, reads with multiple equally good hits were excluded as ambiguous
Insertion locations were aggreagated with gene info using custom PERL scripts
Genome_build: Agrobacterium tumefaciens C58 (consisting of these molecules by Genbank ID: AE007869.2, AE007870.2, AE007871.2, AE007872.2)
Supplementary_files_format_and_content: tab-delimited files with header; file contains number of insertions at a given position in the genome along with annotation information
|
| |
|
| Submission date |
May 04, 2021 |
| Last update date |
Mar 05, 2022 |
| Contact name |
Clay Fuqua |
| E-mail(s) |
cfuqua@indiana.edu
|
| Organization name |
Indiana University
|
| Department |
Biology
|
| Lab |
425E
|
| Street address |
1001 E. Third Street
|
| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47405 |
| Country |
USA |
| |
|
| Platform ID |
GPL30075 |
| Series (1) |
| GSE173827 |
Transposon sequencing for pathway-specific unipolar polysaccharide biosynthesis screen in Agrobacterium tumefaciens C58 |
|
| Relations |
| BioSample |
SAMN19010553 |
| SRA |
SRX10770178 |
